Systems biology is the study of interactions between assorted components of biological systems with the aim of acquiring new insights into how organisms function and respond to different stimuli. Although more and more efforts are being directed toward examining systems biology in complex multi-cellular organisms, the bulk of system-level analyses conducted to date have focused on the biology of microbes. In, Microbial Systems Biology: Methods and Protocols expert researchers in the field describe the utility and attributes of different tools (both experimental and computational) that are used for studying microbial systems. Written in the highly successful Methods in Molecular BiologyTM series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and key tips on troubleshooting and avoiding known pitfalls. Authoritative and practical, Microbial Systems Biology: Methods and Protocols introduces and aids scientists in using the various tools that are currently available for analysis, modification and utilization of microbial organisms.

Microbial mat communities consist of dense populations of microorganisms embedded in exopolymers and/or biomineralized solid phases, and are often found in mm-cm thick assemblages, which can be stratified due to environmental gradients such as light, oxygen or sulfide. Microbial mat communities are commonly observed under extreme environmental conditions, deriving energy primarily from light and/or reduced chemicals to drive autotrophic fixation of carbon dioxide. Microbial mat ecosystems are regarded as living analogues of primordial systems on Earth, and they often form perennial structures with conspicuous stratifications of microbial populations that can be studied in situ under stable conditions for many years. Consequently, microbial mat communities are ideal natural laboratories and represent excellent model systems for studying microbial community structure and function, microbial dynamics and interactions, and discovery of new microorganisms with novel metabolic pathways potentially useful in future industrial and/or medical applications. Due to their relative simplicity and organization, microbial mat communities are often excellent testing grounds for new technologies in microbiology including micro-sensor analysis, stable isotope methodology and modern genomics. Integrative studies of microbial mat communities that combine modern biogeochemical and molecular biological methods with traditional microbiology, macro-ecological approaches, and community network modeling will provide new and detailed insights regarding the systems biology of microbial mats and the complex interplay among individual populations and their physicochemical environment. These processes ultimately control the biogeochemical cycling of energy and/or nutrients in microbial systems. Similarities in microbial community function across different types of communities from highly disparate environments may provide a deeper basis for understanding microbial community dynamics and the ecological role of specific microbial populations. Approaches and concepts developed in highly-constrained, relatively stable natural communities may also provide insights useful for studying and understanding more complex microbial communities.

Microbiologists have become interested in applying "systems biology" to understand and harness complex biological processes in microbial communities. A systems approach, which attempts to use comparative, high-throughput assays, and mathematical or computational models, has been used to generate a picture of system-wide activity that can yield insight into processes operating within a single cell. But the concept of integrating advances in genomics, proteomics, and metabolomics and incorporating them into mathematical models can also be applied to microbial ecosystems, which typically occur in consortia of related and unrelated organisms. Research on microbial communities using a system-based approach could provide a broader perspective on controls on biological processes and how they operate in and among microorganisms. The National Academies of Sciences, Engineering, and Medicine held a workshop on "Progress and Promises of Systems Microbiology" in August 2003, with the intent of providing a forum for discussion of the tools, technology, and programs that are needed to advance the study of microorganisms through a systems approach. Participants also discussed ways to encourage collaboration among scientists of different disciplines. This report summarizes the presentations and discussions from the workshop.

Focusing on the systems biology of bacteria and microorganisms, the 39th volume of Methods in Microbiology investigates the interface between molecular biology, bioinformatics, and modelling and predicting behavior. This cutting-edge research area is of extreme importance to the field and is developing quickly. - Written by research experts in the field - Provides a guide for lab scientists, researchers, and students - Focuses on up-to-date research methods

The 40th volume of Methods in Microbiology focuses on microbial synthetic biology.Synthetic biology is a rapidly growing discipline that builds on well-established principles of genetic engineering and biotechnology by integrating computational and engineering approaches to the design and construction of novel biological systems.This volume addresses some of the major technical challenges stand in the way of achieving a radical step-change in our ability to engineer complex multi-scaled biological systems. These include: the application of computation intelligence to the design of synthetic microbial systems, design automation and constraints; the impact of noise and stochasticity; the engineering of biosensors; the characteristic of a model bacterial chassis. A key issue in Synthetic Biology is that of its social dimensions and a chapter is dedicated to the important issue. - Authority or expertise of contributors - lLnks to websites for the design and modelling of microbes and microbial metabolism - First volume to address the practical issues - Discussion on responsible innovation

Advances in Microbial Physiology is one of the most successful and prestigious series from Academic Press, an imprint of Elsevier. It publishes topical and important reviews, interpreting physiology to include all material that contributes to our understanding of how microorganisms and their component parts work. First published in 1967, it is now in its 64th volume. The Editors have always striven to interpret microbial physiology in the broadest context and have never restricted the contents to “traditional views of whole cell physiology. Now edited by Professor Robert Poole, University of Sheffield, Advances in Microbial Physiology continues to be an influential and very well reviewed series. Contributions from leading authorities Informs and updates on all the latest developments in the field

This volume contains cutting-edge reviews by world-leading experts on the systems biology of microorganisms. As well as covering theoretical approaches and mathematical modelling this book includes case studies on single microbial species of bacteria and archaea, and explores the systems analysis of microbial phenomena such as chemotaxis and phagocytosis. Topics covered include mathematical models for systems biology, systems biology of Escherichia coli metabolism, bacterial chemotaxis, systems biology of infection, host-microbe interactions, phagocytosis, system-level study of metabolism in M.

Many potential applications of synthetic and systems biology are relevant to the challenges associated with the detection, surveillance, and responses to emerging and re-emerging infectious diseases. On March 14 and 15, 2011, the Institute of Medicine's (IOM's) Forum on Microbial Threats convened a public workshop in Washington, DC, to explore the current state of the science of synthetic biology, including its dependency on systems biology; discussed the different approaches that scientists are taking to engineer, or reengineer, biological systems; and discussed how the tools and approaches of synthetic and systems biology were being applied to mitigate the risks associated with emerging infectious diseases. The Science and Applications of Synthetic and Systems Biology is organized into sections as a topic-by-topic distillation of the presentations and discussions that took place at the workshop. Its purpose is to present information from relevant experience, to delineate a range of pivotal issues and their respective challenges, and to offer differing perspectives on the topic as discussed and described by the workshop participants. This report also includes a collection of individually authored papers and commentary.

The book serves as an amalgamation of knowledge and principles used in the area of systems and synthetic biology, and targets inter-disciplinary research groups. The readers from diversified areas would be benefited by the valuable resources and information available in one book. Microbiome projects with efficient data handling can fuel progress in the area of microbial synthetic biology by providing a ready to use plug and play chassis. Advances in gene editing technology such as the use of tailor made synthetic transcription factors will further enhance the availability of synthetic devices to be applied in the fields of environment, agriculture and health. The different chapters of the book reviews a broad range of topics, including food microbiome in ecology, use of microbiome in personalized medicine, machine learning in biomedicine. The book also describes ways to harness and exploit the incredible amounts of genomic data. The book is not only limited to medicine but also caters to the needs of environmentalists, biochemical engineers etc. It will be of interest to advanced students and researchers in life sciences, computational biology, microbiology and other inter-disciplinary areas.